reactomefi's Introduction

Reactome-FI

R Reactome FI Cytoscape plugin wrapper. This package currently implements a limited interface to ReactomeFI functionality including network construction, network clustering, and Pathway/GO term enrichment. It also implements some network plotting capabilities using either sna/ggplot2 or RCytoscape.

Dependencies

plyr
ggplot2
sna
RCurl
XML

Installation

The easiest way to install reactomefi is through devtools:

devtools::install_github("funnell/reactomefi")

Get Started:

network <- ReactomeFINetwork("2012", genes)
annotate(network, "Pathway")
plot(network)

network <- ReactomeFINetwork("2012", genes, cluster=TRUE)
annotateModules(network, "Pathway")
plot(network)

reactomefi's People

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reactomefi's Issues

provide support for new 2013 reactomefi db/api

Handle empty network in ReactomeFINetwork constructor

Right now if the API returns no network an error occurs in the ReactomeFINetwork constructor

provide option to use linker genes

Unit testing with testthat

Clustering Pathway Enrichment Analysis

sna dependency doesn't install automatically

Conversion to Package

Documentation with roxygen2

Reactome FI Pathway Diagram

Using the R cytoscape plugin

Additional Layer of Abstraction to Package

error on no results

Error in [.data.frame(dat, , i) : undefined columns selected
Calls: gene.set.enrichment ... queryAnnotateModules -> df2tsv -> [ -> [.data.frame

need to add tests for cases that return no results at different steps

Pathway Enrichment

Automatically load required packages

ReactomeFINetwork allow imputting pre-computed networks

Somehow allow creating ReactomeFINetwork objects by providing interaction data rather than computing using the API. These networks can then use the clustering and gene set enrichment analysis.

ReactomeFINetwork with use.linkers = TRUE

HI,
I get error with I set use linkers = TRUE for all version. Any suggestion? Thanks Karim

network <- ReactomeFINetwork("2013", GeneList, use.linkers=TRUE )
Opening and ending tag mismatch: HR line 34 and body
Opening and ending tag mismatch: HR line 1 and html
Premature end of data in tag body line 1
Premature end of data in tag html line 1
Error: 1: Opening and ending tag mismatch: HR line 34 and body
2: Opening and ending tag mismatch: HR line 1 and html
3: Premature end of data in tag body line 1
4: Premature end of data in tag html line 1

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